Hi All Just wanted to check on the expected behavior of the summarizeOverlaps function in the GenomicRanges package. 1. In the case of paired end data does it count each read pair as 1 or 2 2. For stranded protocols of RNA-Seq does it take it account the opposite strand of the mate of a read when counting. 3. Also for second strand RNA-Seq where the read 1 matches to the opposite strand of gene will summarizeOverlap work ? Thanks! -Abhi [[alternative HTML version deleted]]